Characterization of Co-transcriptional Formation of G-Quadruplexes in Double-Stranded DNA

2019 ◽  
pp. 243-255
Author(s):  
Ke-wei Zheng ◽  
Jia-yu Zhang ◽  
Zheng Tan
Keyword(s):  
Double Stranded Dna

Optical Absorption Spectroscopy of DNA-Wrapped HiPco Carbon Nanotubes

2019 ◽  
Vol 943 ◽  
pp. 95-99
Author(s):  
Li Jun Wang ◽  
Kazuo Umemura
Keyword(s):  
Carbon Nanotubes ◽  
Aqueous Solution ◽  
Optical Absorption ◽  
Absorption Spectroscopy ◽  
Near Infrared ◽  
Nir Spectroscopy ◽  
Optical Characterization ◽  
Optical Absorption Spectroscopy ◽  
Double Stranded Dna

Optical absorption spectroscopy provides evidence for individually dispersed carbon nanotubes. A common method to disperse SWCNTs into aqueous solution is to sonicate the mixture in the presence of a double-stranded DNA (dsDNA). In this paper, optical characterization of dsDNA-wrapped HiPco carbon nanotubes (dsDNA-SWCNT) was carried out using near infrared (NIR) spectroscopy and photoluminescence (PL) experiments. The findings suggest that SWCNT dispersion is very good in the environment of DNA existing. Additionally, its dispersion depends on dsDNA concentration.

scholarly journals Characterization of a Novel Thermobifida fusca Bacteriophage P318

Viruses ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 1042
Author(s):  
Cheepudom ◽  
Lin ◽  
Lee ◽  
Meng
Keyword(s):  
Plant Cell Wall ◽  
Hydrolytic Enzymes ◽  
Thermobifida Fusca ◽  
Genome Replication ◽  
Putative Orfs ◽  
Base Pairs ◽  
Double Stranded Dna ◽  
Virion Morphogenesis ◽  
Genome Information

Thermobifida fusca is of biotechnological interest due to its ability to produce an array of plant cell wall hydrolytic enzymes. Nonetheless, only one T. fusca bacteriophage with genome information has been reported to date. This study was aimed at discovering more relevant bacteriophages to expand the existing knowledge of phage diversity for this host species. With this end in view, a thermostable T. fusca bacteriophage P318, which belongs to the Siphoviridae family, was isolated and characterized. P318 has a double-stranded DNA genome of 48,045 base pairs with 3′-extended COS ends, on which 52 putative ORFs are organized into clusters responsible for the order of genome replication, virion morphogenesis, and the regulation of the lytic/lysogenic cycle. In comparison with T. fusca and the previously discovered bacteriophage P1312, P318 has a much lower G+C content in its genome except at the region encompassing ORF42, which produced a protein with unknown function. P1312 and P318 share very few similarities in their genomes except for the regions encompassing ORF42 of P318 and ORF51 of P1312 that are homologous. Thus, acquisition of ORF42 by lateral gene transfer might be an important step in the evolution of P318.

scholarly journals Analysis of Ribonucleotide 5′-Triphosphate Analogs as Potential Inhibitors of Zika Virus RNA-Dependent RNA Polymerase by Using Nonradioactive Polymerase Assays

2016 ◽  
Vol 61 (3) ◽  
Author(s):  
Gaofei Lu ◽  
Gregory R. Bluemling ◽  
Paul Collop ◽  
Michael Hager ◽  
Damien Kuiper ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Zika Virus ◽  
Nonstructural Protein ◽  
Rna Dependent Rna Polymerase ◽  
Antiviral Compounds ◽  
Double Stranded Dna ◽  
Virus Rna ◽  
Potential Inhibitors

ABSTRACT Zika virus (ZIKV) is an emerging human pathogen that is spreading rapidly through the Americas and has been linked to the development of microcephaly and to a dramatically increased number of Guillain-Barré syndrome cases. Currently, no vaccine or therapeutic options for the prevention or treatment of ZIKV infections exist. In the study described in this report, we expressed, purified, and characterized full-length nonstructural protein 5 (NS5) and the NS5 polymerase domain (NS5pol) of ZIKV RNA-dependent RNA polymerase. Using purified NS5, we developed an in vitro nonradioactive primer extension assay employing a fluorescently labeled primer-template pair. Both purified NS5 and NS5pol can carry out in vitro RNA-dependent RNA synthesis in this assay. Our results show that Mn2+ is required for enzymatic activity, while Mg2+ is not. We found that ZIKV NS5 can utilize single-stranded DNA but not double-stranded DNA as a template or a primer to synthesize RNA. The assay was used to compare the efficiency of incorporation of analog 5′-triphosphates by the ZIKV polymerase and to calculate their discrimination versus that of natural ribonucleotide triphosphates (rNTPs). The 50% inhibitory concentrations for analog rNTPs were determined in an alternative nonradioactive coupled-enzyme assay. We determined that, in general, 2′-C-methyl- and 2′-C-ethynyl-substituted analog 5′-triphosphates were efficiently incorporated by the ZIKV polymerase and were also efficient chain terminators. Derivatives of these molecules may serve as potential antiviral compounds to be developed to combat ZIKV infection. This report provides the first characterization of ZIKV polymerase and demonstrates the utility of in vitro polymerase assays in the identification of potential ZIKV inhibitors.

scholarly journals Structural studies on M. tuberculosis O6-methylguanine methyltransferase

2014 ◽  
Vol 70 (a1) ◽  
pp. C832-C832
Author(s):  
Menico Rizzi ◽  
Riccardo Miggiano ◽  
Samarpita Lahiri ◽  
Giuseppe Perugino ◽  
Maria Ciaramella ◽  
...  
Keyword(s):  
Excision Repair ◽  
Single Step ◽  
Double Stranded Dna ◽  
Nucleotide Excision ◽  
Enzymatic Systems ◽  
Methylguanine Methyltransferase ◽  
Mutagenic Effects ◽  
Wild Type Form

Mycobacterium tuberculosis (MTB) is an extremely well adapted human pathogen capable to survive for decades inside the hostile environment represented by the host's infected macrophages despite exposure to multiple potential DNA-damaging stresses. In order to maintain a remarkable low level of genetic diversity, MTB deploys different strategies of DNA repair, including multi-enzymatic systems, such as Nucleotide Excision Repair, and single-step repair. In particular, to counteract the mutagenic effects of DNA alkylation, MTB performs the direct alkylated-base reversal by sacrificing one molecule of a DNA-protein alkyltransferase, such as O6-methylguanine methyltransferase (OGT; orf: Rv1316c). We present here the biochemical and structural characterization of recombinant mycobacterial OGT (MtOGT) in its wild-type form along with its mutated variants mimicking the ones occurring in relevant clinical strains (i.e. MtOGT-T15S and MtOGT-R37L). Our studies reveal that MtOGT-R37L is severely impaired in its activity as consequence of its ten-fold lower affinity for modified double-stranded DNA (dsDNA) (1). Further investigations on a new structure-based panel of OGT versions, designed to explore different molecular environment at position 37, allowed us a better understanding of the functional role of the MtOGT Arg37-bearing loop during catalysis. Moreover, we solved the crystal structure of MtOGT in covalent complex with modified dsDNA that reveals an unprecedented MtOGT::DNA architecture, suggesting that the MtOGT monomer performing the catalysis needs assisting unreacted subunits during cooperative DNA binding. This work is supported by European Community FP7 program SYSTEMTB (Health-F4-2010-241587)

scholarly journals Characterization of Two Virulent Phages of Lactobacillus plantarum

2012 ◽  
Vol 78 (24) ◽  
pp. 8719-8734 ◽  
Author(s):  
Mariángeles Briggiler Marcó ◽  
Josiane E. Garneau ◽  
Denise Tremblay ◽  
Andrea Quiberoni ◽  
Sylvain Moineau
Keyword(s):  
Lactobacillus Plantarum ◽  
Corn Silage ◽  
Open Reading Frames ◽  
High Identity ◽  
Content Type ◽  
Defense Systems ◽  
Double Stranded Dna ◽  
Type Phage ◽  
Reading Frames

ABSTRACTWe characterized twoLactobacillus plantarumvirulent siphophages, ATCC 8014-B1 (B1) and ATCC 8014-B2 (B2), previously isolated from corn silage and anaerobic sewage sludge, respectively. Phage B2 infected two of the eightL. plantarumstrains tested, while phage B1 infected three. Phage adsorption was highly variable depending on the strain used. Phage defense systems were found in at least twoL. plantarumstrains, LMG9211 and WCSF1. The linear double-stranded DNA genome of thepac-type phage B1 had 38,002 bp, a G+C content of 47.6%, and 60 open reading frames (ORFs). Surprisingly, the phage B1 genome has 97% identity with that ofPediococcus damnosusphage clP1 and 77% identity with that ofL. plantarumphage JL-1; these phages were isolated from sewage and cucumber fermentation, respectively. The double-stranded DNA (dsDNA) genome of thecos-type phage B2 had 80,618 bp, a G+C content of 36.9%, and 127 ORFs with similarities to those ofBacillusandLactobacillusstrains as well as phages. Some phage B2 genes were similar to ORFs fromL. plantarumphage LP65 of theMyoviridaefamily. Additionally, 6 tRNAs were found in the phage B2 genome. Protein analysis revealed 13 (phage B1) and 9 (phage B2) structural proteins. To our knowledge, this is the first report describing such high identity between phage genomes infecting different genera of lactic acid bacteria.

Characterization of two Salmonella newport bacteriophages

1979 ◽  
Vol 25 (9) ◽  
pp. 1063-1072 ◽  
Author(s):  
N. Moazamie ◽  
H.-W. Ackermann ◽  
M. R. V. Murthy
Keyword(s):  
Molecular Weight ◽  
Melting Point ◽  
Acid Hydrolysis ◽  
Phage Particle ◽  
Size Classes ◽  
Salmonella Newport ◽  
Double Stranded Dna

Salmonella newport phages 16–19 and 7–11 have very long heads and are members of two rare and so far little-known phage groups. Both produce various morphological aberrations. Preparations of phage 7–11 contain numerous polyheads and about 0.4% short heads belonging to nine size classes. In addition, one giant phage particle was observed. The head of phage 7–11 seems to be an icosahedron which became elongated by adding successive rows of subunits. Phages 16–19 and 7–11 have buoyant densities in CsCl of 1.43 and 1.48 g/mL and particle weights of 103 and 204 × 106 respectively. Both viruses contain double-stranded DNA, internal proteins, and sugars. Phage 16–19 contains 46.5% DNA of 35 × 106 molecular weight, and glucose. Phage 7–11 contains 47.5% DNA of 108 × 106 molecular weight, and mannose. Base compositions of phage and S. newport DNAs were determined from buoyant densities, melting point, and acid hydrolysis. Phage 16–19 contains 5.4% 5-methylcytosine.

Isolation and characterization of two new Staphylococcus aureus bacteriophages with potential to infect distinct bacteria from bovine mastitis

2021 ◽  
Author(s):  
Bibiana Martins Barasuol ◽  
Juliana Felipetto Cargnelutti ◽  
Luis Antônio Sangioni ◽  
Daniela Isabel Brayer Pereira ◽  
Ana Paula Muterle Varela ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Bovine Milk ◽  
Bovine Mastitis ◽  
Gc Content ◽  
Etiologic Agent ◽  
Cure Rate ◽  
Long Tail ◽  
Isolation And Characterization ◽  
Double Stranded Dna

Abstract Bovine mastitis is an important disease of dairy cows, and Staphylococcus aureus is the etiologic agent most prevalent among the microorganisms. Mastitis caused by S. aureus present low cure rate with antimicrobials treatment and low vaccines efficacy. Bacteriophages or phages have been considered as an alternative for treating this disease. This study, we isolated and characterized two new S. aureus phages, namely B_UFSM4 and B_UFSM5, from bovine milk of cows with mastitis. The adsorptions rates were 10–20 min for B_UFSM4 and 20–30 min for B_UFSM5. Phages activities were relatively stable at pH 3–11; however, at temperatures of 50 °C-60ºC-70ºC/60 min, the phages were completely inactivated. These viruses presented infectivity in various bacteria isolated from bovine mastitis, where the lytic activity of phages B_UFSM4 and B_UFSM5 were 34.2%(13/38) and 42.1%(16/38), respectively, including isolates from S. aureus, Pseudomonas aeruginosa, Staphylococcus sciuri, and Rothia terrae. The complete genomes of B_UFSM4 and B_UFSM5 have 41.396 bp and 41.829 bp, with GC-content 33.97% and 33.98%, respectively. Both phages comprise 61 putative ORFs. The viruses have double stranded DNA and linear architecture. Phylogenic similarity was observed by proteome with Staphylococcus prophage phiPV83 (45,536 nt), Staphylococcus phage CN125 (44,492 nt) and Staphylococcus phage JS01 (43,458 nt). Based on the morphology, the phages belong to Siphoviridae family, presenting icosahedral head with a long tail, Caudovirales order and Biseptimavirus genus. Thus, two S. aureus phages (B_UFSM4 and B_UFSM5) were isolated and characterized, and these phages can be used as therapeutic or prophylactic candidates against S. aureus infections in cattle mastitis.

Preparation and characterization of pyrene modified uridine derivatives as potential electron donors in RNA

2018 ◽  
Vol 16 (41) ◽  
pp. 7663-7673 ◽  
Author(s):  
Jennifer Frommer ◽  
Beatrice Karg ◽  
Klaus Weisz ◽  
Sabine Müller
Keyword(s):  
Charge Transfer ◽  
Electron Donors ◽  
Double Stranded Dna ◽  
The Subject

Charge transfer across double stranded DNA has been the subject of a large number of studies, whereas RNA has been hardly investigated in this regard.

Characterization of Marine Temperate Phage-Host Systems Isolated from Mamala Bay, Oahu, Hawaii

1998 ◽  
Vol 64 (2) ◽  
pp. 535-542 ◽  
Author(s):  
Sunny C. Jiang ◽  
Christina A. Kellogg ◽  
John H. Paul
Keyword(s):  
Water Samples ◽  
Blot Hybridization ◽  
Temperate Phage ◽  
Dot Blot ◽  
Dot Blot Hybridization ◽  
Double Stranded Dna ◽  
The Family ◽  
Marine Viruses

ABSTRACT To understand the ecological and genetic role of viruses in the marine environment, it is critical to know the infectivity of viruses and the types of interactions that occur between marine viruses and their hosts. We isolated four marine phages from turbid plaques by using four indigenous bacterial hosts obtained from concentrated water samples from Mamala Bay, Oahu, Hawaii. Two of the rod-shaped bacterial hosts were identified as Sphingomonas paucimobilis andFlavobacterium sp. All of the phage isolates were tailed phages and contained double-stranded DNA. Two of the phage isolates had morphologies typical of the family Siphoviridae, while the other two belonged to the families Myoviridae andPodoviridae. The head diameters of these viruses ranged from 47 to 70.7 nm, and the tail lengths ranged from 12 to 146 nm. The burst sizes ranged from 7.8 to 240 phage/bacterial cell, and the genome sizes, as determined by restriction digestion, ranged from 36 to 112 kb. The members of the Siphoviridae, T-φHSIC, and T-φD0, and the member of the Myoviridae, T-φD1B, were found to form lysogenic associations with their bacterial hosts, which were isolated from the same water samples. Hybridization of phage T-φHSIC probe with lysogenic host genomic DNA was observed in dot blot hybridization experiments, indicating that prophage T-φHSIC was integrated within the host genome. These phage-host systems are available for use in studies of marine lysogeny and transduction.

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